Article
Cell Biology
Vytaute Boreikaite, Thomas S. Elliott, Jason W. Chin, Lori A. Passmore
Summary: In this study, the researchers reconstituted the 3' endonuclease activity of human CPSF and identified the protein factors required for this activity. They found that the activation and site-specific pre-mRNA cleavage by CPSF are tightly controlled. The results suggest that fidelity in mRNA processing is maintained through precise regulation of CPSF activity.
GENES & DEVELOPMENT
(2022)
Editorial Material
Cell Biology
Yoseop Yoon, Yongsheng Shi
Summary: In this article, two independent studies successfully reconstituted the processing of human pre-mRNA 3' ends using defined components in vitro. These studies are of great importance for understanding the nature and essential components of this biological process.
GENES & DEVELOPMENT
(2022)
Article
Multidisciplinary Sciences
Buki Kwon, Mervin M. Fansler, Neil D. Patel, Jihye Lee, Weirui Ma, Christine Mayr
Summary: Multi-UTR genes express their alternative 3' UTR isoforms in a cell type-specific manner. Transcriptional enhancers, along with transcription factors, regulate the expression of these isoforms by influencing the cleavage activity of polyadenylation sites.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Wei Zhang, Yaoqin Mu, Kejun Dong, Lei Zhang, Bei Yan, Hao Hu, Yangwei Liao, Rong Zhao, Wan Shu, Zhengxin Ye, Yaping Lu, Chong Wan, Qiangqiang Sun, Longjie Li, Hongbo Wang, Xianjin Xiao
Summary: This study discovered a new targeting substrate for LbaCas12a and its special enzymatic properties for dsDNA with a sticky-end region. The study also demonstrated the low-temperature activation of CRISPR-Cas12a and developed a complete workflow for low-abundance point mutation detection in real samples.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Pedro A. Gutierrez, Kirk Baughman, Yadong Sun, Liang Tong
Summary: CPSF73 is an endonuclease that catalyzes the cleavage reaction for 3'-end processing of mRNA precursors in two distinct machineries. Recent studies suggest that CPSF73 is a potential target for developing anticancer, antimalarial, and antiprotozoal drugs. By developing a real-time fluorescence assay, the nuclease activity of CPSF73 can be efficiently measured.
Article
Biochemistry & Molecular Biology
Chuande Wang, Martine Quadrado, Hakim Mireau
Summary: Initiation and termination of plant mitochondrial transcription are poorly controlled. 3 ' -end processing and control of RNA stability are important for mature mRNA production in plant mitochondria. A study showed that the PPR protein EMS1 is essential for the production and stabilization of a specific transcript, nad2 exons 1-2, in plant mitochondria. It was found that EMS1 plays a role in both blocking exonucleolytic activity and endonucleolytic cleavage for 3 ' end formation of this transcript.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Yang Liu, Filipe Pinto, Xinyi Wan, Zhugen Yang, Shuguang Peng, Mengxi Li, Jonathan M. Cooper, Zhen Xie, Christopher E. French, Baojun Wang
Summary: This study reveals the programmability of crRNA-tracrRNA hybridization in type II CRISPR systems. By reprogramming the crRNA-tracrRNA interactions, the researchers demonstrate the design of orthogonal cellular computing devices and the hijacking of endogenous small RNAs/mRNAs as crRNAs. Furthermore, they demonstrate the use of re-engineered gRNA pairings as RNA sensors for monitoring gene transcription or detecting SARS-CoV-2 RNA.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Megumi Endo, Jung In Kim, Narumi Aoki Shioi, Shigenori Iwai, Isao Kuraoka
Summary: Endonuclease V is highly conserved across species and can cleave DNA and RNA containing inosine. AtEndoV in Arabidopsis thaliana exhibits variations in substrate specificity and prefers RNA over DNA substrates. This suggests that AtEndoV functions in processing RNA substrates with inosine induced by RNA damage, rather than A-to-I RNA editing.
Article
Biochemistry & Molecular Biology
Neha Nagpal, Albert K. Tai, Jayakrishnan Nandakumar, Suneet Agarwal
Summary: Mutations in the DKC1 gene lead to abnormalities in scaRNA13, which can be restored by gene editing to repair mutations or inhibition of relevant enzymes; additionally, it was found that the NTE plays an important role in regulating the 3' end definition of snoRNA.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Zhihao Wang, Hongliang Wang, Nancy Mulvenna, Maximo Sanz-Hernandez, Peipei Zhang, Yanqing Li, Jia Ma, Yawen Wang, Steve Matthews, Sivaramesh Wigneshweraraj, Bing Liu
Summary: Proteins mimic DNA to occupy DNA binding sites, preventing further access. The phage protein Gp44 employs this strategy to inhibit host RNA polymerase, leading to bacterial growth inhibition. This non-specific strategy may have potential applications in developing genetically engineered phages for phage therapy targeting a range of bacterial hosts.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yao Wang, Tao Qi, Jingtong Liu, Yuan Yang, Ziwen Wang, Ying Wang, Tianyi Wang, Miaomiao Li, Mingqing Li, Daru Lu, Alex Chia Yu Chang, Li Yang, Song Gao, Yongming Wang, Feng Lan
Summary: The CRISPR-Cas system can treat autosomal dominant diseases by disrupting mutant alleles through nonhomologous end joining (NHEJ). However, current CRISPR-Cas systems cannot differentiate many single-nucleotide mutations from wild-type alleles. We identified Cas12j-8 as an ideal genome editor with comparable activity to AsCas12a and Un1Cas12f1. Cas12j-8 is a highly specific nuclease sensitive to single-nucleotide mismatches in the protospacer adjacent motif (PAM)-proximal region. It enables allele-specific disruption of genes with single-nucleotide polymorphisms (SNPs) and has potential therapeutic applications.
Article
Chemistry, Analytical
Qinli Pu, Hongyan Yu, Xi Zhou, Junjie Li, Yujun Yang, Ting Wang, Fugang Li, Shangchun Sheng, Guoming Xie
Summary: The study proposes a simple XNA probe for directly amplifying the minor differences between epigenetic bases and unmodified bases in RNA through mediating m6A-specific reverse transcription quantitative polymerase chain reaction (MsRT-qPCR). This method allows for the quantification of multiple specific m6A sites in mRNA and lncRNA samples.
Article
Medicine, Research & Experimental
Kyung Hyun Lee, Seongcheol Kim, Jaehwi Song, Seung Ryul Han, Ji Hyun Kim, Seong-Wook Lee
Summary: In this study, a new in vitro circRNA engineering method was developed, which effectively generates highly useful circRNAs. This method does not introduce any extraneous fragments and avoids unwanted immune responses in cells. The generated circRNA can be efficiently purified and used for cell-based analysis. It exhibits stable protein expression and does not induce innate immune responses.
MOLECULAR THERAPY NUCLEIC ACIDS
(2023)
Article
Chemistry, Medicinal
Zenon Konteatis, Jeremy Travins, Stefan Gross, Katya Marjon, Amelia Barnett, Everton Mandley, Brandon Nicolay, Raj Nagaraja, Yue Chen, Yabo Sun, Zhixiao Liu, Jie Yu, Zhixiong Ye, Fan Jiang, Wentao Wei, Cheng Fang, Yi Gao, Peter Kalev, Marc L. Hyer, Byron DeLaBarre, Lei Jin, Anil K. Padyana, Lenny Dang, Joshua Murtie, Scott A. Biller, Zhihua Sui, Kevin M. Marks
Summary: This study reports the discovery of highly potent, selective MAT2A inhibitors that overcome previous challenges in targeting MAT2A. Through fragment screening and structure-guided design, these inhibitors significantly reduce SAM levels in cancer cells and selectively block proliferation of MTAP-null cells.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Clinical Neurology
Chaker Aloui, Dominique Herve, Gaelle Marenne, Florian Savenier, Kilan Le Guennec, Francoise Bergametti, Edgard Verdura, Thomas E. Ludwig, Jessica Lebenberg, Waliyde Jabeur, Helene Morel, Thibault Coste, Genevieve Demarquay, Panagiotis Bachoumas, Julien Cogez, Guillaume Mathey, Emilien Bernard, Hugues Chabriat, Emmanuelle Genin, Elisabeth Tournier-Lasserve
Summary: This study identified LAMB1 truncating variants that are strongly overrepresented in CSVD patients, associated with a novel phenotype characterized by the combination of a hippocampal-type episodic memory defect and diffuse vascular leukoencephalopathy.
ANNALS OF NEUROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Benjamin G. G. Saward, Thomas M. M. Leissing, Ian J. J. Clifton, Anthony Tumber, Christopher M. M. Timperley, Richard J. J. Hopkinson, Christopher J. J. Schofield
Summary: Transient receptor potential (TRP) channels play important roles in environmental sensing in animals. TRPA1 is responsible for sensing AITC and other electrophilic irritants, while TRPV3 is involved in skin maintenance. This study reports on the catalysis of asparaginyl hydroxylation of the ankyrin repeat domains (ARDs) of TRPA1 and TRPV3 by FIH. The results confirm previous findings on TRPV3 hydroxylation and identify a specific sequence in TRPA1 that undergoes hydroxylation. Structural studies reveal similarities and differences in the binding modes of TRPA1 and TRPV3 to FIH.
Article
Multidisciplinary Sciences
Ryan A. Herold, Raphael Reinbold, Christopher J. Schofield, Fraser A. Armstrong
Summary: Electrochemical studies reveal that nanoconfinement significantly increases the efficiency of enzyme-catalyzed cascade reactions. By using a nanoporous conducting indium tin oxide film and entrapping Isocitrate dehydrogenase 1 (IDH1), the complete electrochemical oxidation of isocitrate to 2-oxoglutarate is achieved using only the NADP(H) cofactor carried into the electrode pores. The results demonstrate the power of nanoconfinement in facilitating multistep enzyme catalysis and provide insights into the role of nicotinamide cofactors as redox carriers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Vildan A. Turkmen, Jordi C. J. Hintzen, Anthony Tumber, Laust Moesgaard, Eidarus Salah, Jacob Kongsted, Christopher J. Schofield, Jasmin Mecinovic
Summary: Non-haem Fe(ii) and 2-oxoglutarate (2OG) dependent oxygenases catalyze oxidation of proteins, and this study focuses on the substrate selectivity and inhibition of human ribosomal oxygenases (ROX) MINA53 and NO66. The results show that MINA53 and NO66 have narrow substrate selectivity compared to other human JmjC hydroxylases. Inhibition assays also suggest that the activities of MINA53/NO66 might be regulated in vivo by competition with non-oxidized proteins/peptides.
RSC CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Medicinal
Shuang Liu, Martine Abboud, Victor Mikhailov, Xiao Liu, Raphael Reinbold, Christopher J. Schofield
Summary: This study reported the binding and inhibition studies of 13 IDH1/2 variant inhibitors on wild-type IDH1 and its cancer-associated variant, IDH1 R132H. Interestingly, all the variant inhibitors were able to bind wild-type IDH1 despite not inhibiting it or only weakly inhibiting it. The selectivity of the IDH1 R132H variant over wild-type IDH1 is not primarily related to the affinities of the inhibitors for the resting forms of the enzymes. The independent binding of Mg2+ and 2-oxoglutarate to the IDH1 variant makes it more susceptible to allosteric inhibition compared to the tighter binding of the isocitrate-Mg2+ complex substrate to wild-type IDH1. The results highlight that binding affinity does not necessarily correlate with inhibition selectivity and have implications for interpreting inhibitor screening results with IDH and related enzymes.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Plant Sciences
Daniela J. Sueldo, Alice Godson, Farnusch Kaschani, Daniel Krahn, Till Kessenbrock, Pierre Buscaill, Christopher J. Schofield, Markus Kaiser, Renier A. L. van Der Hoorn
Summary: This study reports the dynamics of extracellular hydrolases in Nicotiana benthamiana upon infection with Pseudomonas syringae. The activity of 82 hydrolases, mostly serine hydrolases, increases during infection, while the activity of 60 hydrolases, mostly glycosidases and cysteine proteases, is suppressed. The study also reveals the antibacterial activity of NbPR3 and its essential active site substitution.
Article
Multidisciplinary Sciences
Vijil Chenthamarakshan, Samuel C. Hoffman, C. David Owen, Petra Lukacik, Claire Strain-Damerell, Daren Fearon, Tika R. Malla, Anthony Tumber, Christopher J. Schofield, Helen M. E. Duyvesteyn, Wanwisa Dejnirattisai, Loic Carrique, Thomas S. Walter, Gavin R. Screaton, Tetiana Matviiuk, Aleksandra Mojsilovic, Jason Crain, Martin A. Walsh, David I. Stuart, Payel Das
Summary: We validate the broad utility of a deep generative framework trained on protein sequences, small molecules, and their interactions to discover inhibitors for emerging drug-target proteins. By using protein sequence-conditioned sampling, we successfully designed small-molecule inhibitors for two dissimilar targets without knowing their structures or active molecules. In vitro experiments showed micromolar-level inhibition for two out of four synthesized candidates for each target. The most potent inhibitor also exhibited activity against several variants in live virus neutralization assays, demonstrating the effectiveness and efficiency of the generative foundation model in accelerated inhibitor discovery without target structure or binder information.
Article
Chemistry, Multidisciplinary
H. T. Henry Chan, A. Sofia F. Oliveira, Christopher J. Schofield, Adrian J. Mulholland, Fernanda Duarte
Summary: The SARS-CoV-2 main protease (M-pro) is crucial in the coronavirus lifecycle by breaking down viral polyproteins. This study used dynamical nonequilibrium molecular dynamics (D-NEMD) simulations to examine the behavior of M-pro with and without substrates. The results reveal communication between M-pro subunits and identify networks associated with allosteric inhibition and nirmatrelvir resistance. These findings suggest that certain mutations can lead to drug resistance by altering the allosteric behavior of M-pro. Overall, the study demonstrates the usefulness of D-NEMD in identifying functionally relevant allosteric sites and networks, including those relevant to drug resistance.
Article
Chemistry, Multidisciplinary
Ryan A. Herold, Christopher J. Schofield, Fraser A. Armstrong
Summary: The study utilizes a nanoporous electrode material, the e-Leaf, to control enzyme cascades and gain detailed kinetic insight into an anti-cancer drug mechanism. The e-Leaf allows for the quantification of IDH1 R132H inhibition kinetics and reveals factors underlying inhibitor residence time. The study highlights the importance of this method in obtaining detailed kinetic and mechanistic information that is difficult to obtain using conventional techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
David J. Fallon, Alex Phillipou, Christopher J. Schofield, David House, Nicholas C. O. Tomkinson, Jacob T. Bush
Summary: This article presents the development and optimization of a photoaffinity labelling (PAL) displacement assay. It uses a highly efficient PAL probe to assess the relative binding affinities of compounds to specific binding sites in multiple recombinant protein domains in tandem. The assay was validated using a test set of 264 compounds annotated with activity against the bromodomain and extra-terminal domain (BET) family in ChEMBL. The obtained pIC50 values correlated well with orthogonal TR-FRET data, highlighting the potential of this accessible PAL biochemical screening platform.
BIOCHEMICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Lennart Brewitz, H. T. Henry Chan, Petra Lukacik, Claire Strain-Damerell, Martin A. Walsh, Fernanda Duarte, Christopher J. Schofield
Summary: This study investigates the DUB activity of PLpro and confirms its activity using mass spectrometry. The results suggest that the sequence and binding of substrates affect the catalysis of PLpro, and human proteins conjugated to ISG15 are better substrates. The study also implies the potential of using N epsilon-lysine-branched oligopeptides for substrate identification and monitoring catalysis by human DUBs.
BIOORGANIC & MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Inna Zukher, Gwendal Dujardin, Rui Sousa-Luis, Nick J. Proudfoot
Summary: This study demonstrates the role of non-cleaving Cas9 (dCas9) in transcriptional regulation, showing its ability to precisely control RNA polymerase II transcriptional pausing and termination, with minimal effects on alternative splicing.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
William D. Figg Jr, Giorgia Fiorini, Rasheduzzaman Chowdhury, Yu Nakashima, Anthony Tumber, Michael A. McDonough, Christopher J. Schofield
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biology
Onofrio Zanin, Matthew Eastham, Kinga Winczura, Mark Ashe, Rocio T. Martinez-Nunez, Daniel Hebenstreit, Pawel Grzechnik
Summary: The presence of the cap is crucial for initiating the degradation of mRNA, and the levels of non-capped mRNA are inversely correlated with their expression levels.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anthony Tumber, Eidarus Salah, Lennart Brewitz, Thomas P. Corner, Christopher J. Schofield
Summary: Jumonji-C (JmjC) domain-containing protein 5 (JMJD5) is an oxygenase linked to circadian rhythm and cancer biology. Synthetic 2OG derivatives with cyclic carbon backbones are alternative cosubstrates of JMJD5, demonstrating structural similarity to factor inhibiting hypoxia-inducible transcription factor HIF-a (FIH). Broad-spectrum 2OG oxygenase inhibitors are also efficient JMJD5 inhibitors, while clinical inhibitors like roxadustat do not inhibit JMJD5. Solid phase extraction coupled to mass spectrometry assays will facilitate the development of selective JMJD5 inhibitors for cellular studies.
RSC CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
H. T. Henry Chan, Lennart Brewitz, Petra Lukacik, Claire Strain-Damerell, Martin A. Walsh, Christopher J. Schofield, Fernanda Duarte
Summary: This study investigates how SARS-CoV-2 PLpro binds viral polyprotein-derived oligopeptide substrates through molecular dynamics, docking, and quantum mechanics/molecular mechanics calculations. The results show that a proline located at the P2' position promotes catalysis.
RSC CHEMICAL BIOLOGY
(2023)
